Issue #29 resolved

Issue parsing this molecule

Anonymous created an issue

I try to use opsin to convert this molecule name into smile:

acetic acid 2'-methyl-2'-(1",2",4"-trimethylpent-2"-enyloxy)propyl ester

can you tell me why it does not work ?

best regard,

Guillaume Godin

Comments (3)

  1. guillaume godin

    I try removing all the ' & '' and it works: acetic acid 2-methyl-2-(1,2,4-trimethylpent-2-enyloxy)propyl ester CC(COC(C)=O)(C)OC(C(=CC(C)C)C)C

    Is it possible to accept those ' & '' values in the input name ?

    Guillaume GODIN

  2. Daniel Lowe repo owner

    Hi Guillaume, As you correctly spotted OPSIN does not like the additional primes which as you can see from your simplified name are redundant.

    The logic behind the primes is somewhat like http://www.acdlabs.com/iupac/nomenclature/79/r79_36.htm Rule 2.5b (which OPSIN does not currently implement, mainly as names constructed in this manner are very rare, and this rule does not appear in more recent IUPAC recommendations)... but the combination of primes to indicate level of branching and brackets is idiosyncratic.

    Do you where the name came from? Some name to structure algorithms, like ChemDraw's are quite sloppy about primes (as long as all locants referring to the same group have the same number of primes) and will accept the name, but unless the issue is common I prefer to be strict.

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